You're not missing anything. The artist didn't understand the difference between fenceposts and fence, boundary and interior.
When presented with beautiful evidence of his mistake, he failed to see what it was showing him.
The art is good in that it's a puzzle to interpret the mistake and resolve the paradox, even if (especially if!) the artist doesn't understand what they created.
> "What I had stumbled upon was that physical entities (stones) are not equatable with conceptual entities (points)," Bochner said
That's because the relevant conceptual and physical entities when contemplating lengths of sides of triangles, which is what Pythagoras' theorem is about, are lines, not points.
>The artist claims it was intentional. Do you know otherwise?
His reply reveals that he still doesn't get it, which to me seems to prove that it can't have been intentional.
When presented with beautiful evidence of his mistake, he failed to see what it was showing him.
The art is good in that it's a puzzle to interpret the mistake and resolve the paradox, even if (especially if!) the artist doesn't understand what they created.